An Interview with Alan Gelfand

David Warton interviews Alan Gelfand, a keynote speaker at the Statistics in Ecology and Environmental Monitoring (SEEM) conference in Queenstown, NZ. Alan is best known for proposing Bayesian estimation of a posterior distribution using Gibbs sampling, in his classic papers ‘Sampling-Based Approaches to Calculating Marginal Densities‘ and ‘Illustration of Bayesian Inference in Normal Data Models Using Gibbs Sampling‘.

David and Alan discuss the origins of the idea that revolutionised Bayesian statistics, Alan’s current research, and his passion for ecology.

Check out David’s other interviews on the Methods in Ecology and Evolution YouTube channel.


Practical Tools: A New Article Type and a Virtual Issue

Today, we’re pleased to announce that we’re launching a new article type for Methods in Ecology and Evolution: Practical Tools. Like our Applications articles, Practical Tools will be short papers (up to 3000 words). They’ll focus on new field techniques, equipment or lab protocols. From this point forward, our Applications papers will solely focus on software and code.

Practical tools need to clearly demonstrate how tools designed for specific systems or problems can be adapted for more general use. Online supporting information can include specific instructions, especially for building equipment. You can find some examples of Applications that would now fit into this article type here and here.

To help launch our new article type, we asked four of our Associate Editors – Pierre Durand, Graziella Iossa, Nicolas Lecomte and Andrew Mahon – to put together a Virtual Issue of papers about Field Methods that have previously been published in the journal. All of the articles in ‘Practical Tools: A Field Methods Virtual Issue‘ will be free to everyone for the next month. You can find out a bit more about each of the four sections of the Virtual Issue below. Continue reading

ANDe™: High‐Throughput eDNA Sampling in a Fully Integrated System

Current eDNA sampling technologies consist mainly of do‐it‐yourself solutions. The lack of purpose‐built sampling equipment is limiting the efficiency and standardization of eDNA studies. So, Thomas et al. (a team of molecular ecologists and engineers) designed ANDe™.

In this video, the authors highlight the key features and benefits of ANDe™. This integrated system includes a backpack-portable pump that integrates sensor feedback, a pole extension with remote pump controller, custom‐made filter housings in single‐use packets for each sampling site and on-board sample storage. 

This video is based on the article ‘ANDe: A fully integrated environmental DNA sampling system‘ by Thomas et al.

Virtually Trekking Across the Pond with the Newest Senior Editor: Aaron M. Ellison

Post Provided by Aaron Ellison

I’m delighted to be the newest member of the diverse team of Senior and Associate Editors who have made Methods in Ecology and Evolution one of the premier journals in the field. After 15 years working on the lead editorial teams of Ecology and Ecological Monographs, I’m really looking forward to applying my editorial energies to the ESA’s friendly competitor on the other side of the ‘pond’.

My background includes:

  • an undergraduate degree in East Asian Philosophy
  • a PhD in evolutionary ecology
  • research and teaching on the natural history and population, community, and landscape ecology of plants and animals (mostly invertebrates) in the marine intertidal and subtidal, among salt marshes and mangroves, tropical and temperate forests, and carnivorous plant bogs
  • extensive forays into statistics, mathematics, and software engineering
  • increasing attention to the history and practice of art and architecture and their relationship to ecological theory
  • a quirky social-media persona
  • and more than two decades of work in editing and publishing journals with scientific societies.

All of these things contribute to my open, catholic approach to scientific research, teaching, and publishing, and their relationship to the broader world.

The editors of Methods are always interested in seeing papers on methodological advances and approaches that lead to new directions. We love reading about creative solutions for new challenges in ecological and evolutionary research and applications in the broadest sense. As a new Senior Editor, I’m especially hoping to encourage more papers in three areas: field methods (about which I’ve published two of my own papers in Methods), reproducibility, and science communication. Continue reading

2017 Robert May Prize Winner: Jonathan Henshaw

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2017 winner is Jonathan Henshaw, for his article ‘A unified measure of linear and nonlinear selection on quantitative traits.

The standard approach to quantifying natural selection, developed by Lande and Arnold, does not allow for comparable metrics between linear (i.e. selection on the mean phenotype) and nonlinear (i.e. selection on all other aspects of the phenotypic distribution, including variance and the number of modes) selection gradients. Jonathan Henshaw’s winning submission provides the first integrated measure of the strength of selection that applies across qualitatively different selection regimes (e.g. directional, stabilizing or disruptive selection). Continue reading

Issue 9.2

Issue 9.2 is now online!

The February issue of Methods is now online!

This double-size issue contains six Applications articles (one of which is Open Access) and two Open Access research articles. These eight papers are freely available to everyone, no subscription required.

 Temperature Manipulation: Welshofer et al. present a modified International Tundra Experiment (ITEX) chamber design for year-round outdoor use in warming taller-stature plant communities up to 1.5 m tall.This design is a valuable tool for examining the effects of in situ warming on understudied taller-stature plant communities

 ZoonThe disjointed nature of the current species distribution modelling (SDM) research environment hinders evaluation of new methods, synthesis of current knowledge and the dissemination of new methods to SDM users. The zoon R package aims to overcome these problems by providing a modular framework for constructing reproducible SDM workflows.

 BEIN R Package: The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented wealth of cleaned and standardised botanical data. The bien r package allows users to access the multiple types of data in the BIEN database. This represents a significant achievement in biological data integration, cleaning and standardisation.

Continue reading

An Interview with Tony Ives

David Warton interviews Tony Ives, a Keynote speaker at the Statistics in Ecology and Environmental Monitoring (SEEM) conference in Queenstown, NZ. Tony has published a few papers in Methods in Ecology and Evolution over the last couple of years – first we discuss the exchanges on log-transformation of counts (including a paper co-authored with David Warton).

Tony and David then talk about a recent paper by Daijiang Li with Tony, on the need to check for phylogenetic structure when looking for associations between species trait and the environment.

We’ll have more of David’s interviews from the SEEM Conference coming out over the next couple of months. Keep an eye out for them here and on the Methods in Ecology and Evolution YouTube channel.

New Associate Editor: Chris Sutherland

Today, we are pleased to welcome the latest new member of the Methods in Ecology and Evolution Associate Editor Board. Chris Sutherland joins us from the University of Massachusetts, USA and you can find out a little more about him below.

Chris Sutherland

“I’m an applied ecologist with a focus on spatial population ecology. I am particularly interested in understanding how spatial processes such as movement, dispersal and connectivity, influence the dynamics of spatially structured populations. Most of my research involves the development and application of spatially realistic hierarchical models for observations of individuals, populations and metapopulations.”

Chris has had a couple of articles published in Methods in Ecology and Evolution in recent years. In his 2015 article ‘Modelling non-Euclidean movement and landscape connectivity in highly structured ecological networks‘ Chris and his co-authors (Angela K. Fuller and J. Andrew Royle) evaluated the consequences of not accounting for movement heterogeneity when estimating abundance in highly structured landscapes, and demonstrated the value of this approach for estimating biologically realistic space-use patterns and landscape connectivity.

A multiregion community model for inference about geographic variation in species richness‘ by Chris, Mattia Brambilla, Paolo Pedrini and Simone Tenan was published in the journal in 2016. This paper reported on a new approach that provided a mechanism for testing hypotheses about why and how species richness varies across space.

Last year, Chris was also involved in ‘Quantifying spatial variation in the size and structure of ecologically stratified communities‘, which was published in the August issue of Methods. In this article, the authors provided a novel hierarchical multi-region community model for direct modelling of trait-based patterns of species richness along environmental gradients by splitting communities into ecologically relevant strata.

Chris currently has a number of ongoing projects including a long term (20 year) metapopulation study on water voles in North West Scotland with the objectives of better understanding the spatial drivers of colonisation-extinction dynamics and persistence of spatially structured populations. He is also working on monitoring and density estimation of a recovering population of American marten using photographic capture-recapture using a novel camera trapping design.

We are thrilled to welcome Chris as a new Associate Editor and we look forward to working with him on the journal.

Policy on Publishing Code: Encouraging Good Practice to Ensure Quality

Following on from our sponsorship of the Guide to Reproducible Code in Ecology and Evolution and our collaboration with rOpenSci, we have now released a new policy on publishing code. The main objective of this policy is to make sure that high quality code is readily available to our readers.

We’ve set out four key principles to help achieve this, as well as explaining what code outputs we publish, giving some examples of things that make it easier to review code, and giving some advice on how to store code once it’s been published. Below is a summary of some highlights of the policy, but you can find it in full on the Methods in Ecology and Evolution website. Continue reading

New Studies Aim to Boost Social Science Methods in Conservation Research

Below is a press release about the Methods Special Feature ‘Qualitative Methods for Eliciting Judgements for Decision Making‘ taken from the University of Exeter.

Scientists have produced a series of papers designed to improve research on conservation and the environment.

A group of researchers have contributed to a Special Feature of the journal Methods in Ecology and Evolution to examine commonly used social science techniques and provide a checklist for scientists to follow.

Traditional conservation biology has been dominated by quantitative data (measured in numbers) but today it frequently relies on qualitative methods such as interviews and focus group discussions. The aim of the special issue is to help researchers decide which techniques are most appropriate for their study, and improve the “methodological rigour” of these techniques. Continue reading